January 2006 - modeller_usage

fix_offsets to align certain residues
by jf163201＠ohio.edu 30 Jan '06

30 Jan '06

Hi, I'm trying to figure out how to use fix_offsets with align2d. Please follow this example, based on the salign() example (under the 'Alignments using external restraints subsection') in the manual. Here is the input file, fix_positions.ali >P1;1abc sequence:1abc:1::10:: : :-1.00:-1.00 FGAVAFATTT* >P1;1def sequence:1def: :: :: : :-1.00:-1.00 AVAFATTT* >P1;_fix_pos sequence:x: :: :: : :-1.00:-1.00 0000000000* Following is the .py file. I've removed the comments but it's taken directly from the manual log.verbose() env = environ() aln = alignment(env, file='fix_positions.ali', align_codes=('1abc', '1def', '_fix_pos')) aln.salign(fix_offsets=(0, 1000, 2000, 3000, 4000), gap_penalties_2d=(0, 0, 0, 0, 0, 0, 0, 0, 0), # Any values are # possible here local_alignment=False, # Local alignment works, too gap_penalties_1d=(-600, -400)) # This is best with the default value # of gap_penalties_2d aln.write(file='fix_positions_salign.pap', alignment_format='PAP') If I run this, I will get an alignment of: _aln.pos 10 1abc FGAVAFATTT 1def --AVAFATTT _consrvd ******** But suppose I want to force the first Alanine in 1abc to be aligned with the 2nd Alanine in 1def. I want modeller to align all other residues normally (as it normally would without any fix_offsets). So I want something that would _probably_ look like this: _aln.pos 10 1abc FGAVAFATTT 1def AVA--FATTT _consrvd ******** The only thing that matters is that the first A in 1abc is forced to align with the 2nd A in 1def. How do I get these particular Ala residues to be forced to align using _fix_pos input in the alignment file? Specifically, what would I need to put in place of the zeros below? >P1;_fix_pos sequence:x: :: :: : :-1.00:-1.00 0000000000* I've been playing around with it but can't seem to get it work correctly. To ask the question a different way, given two sequnces, A and B, how does one tell Modeller the residue #X of sequence A must be aligned with residue #Y of sequence B. Thank you, Jim Fonseca

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problem with ligand attachment
by Natasha Khan 30 Jan '06

30 Jan '06

Hello I am trying to attach hetatoms*(4 Mn,4 Mg,4 NAD, and 1027 water molecules)* to my model(an enzyme) using mod8v1,but somehow I always fail to get the output files(*B9999?????* *and the V9999???? files *).I do get the other output files*(D00000?????,.ini,.rsr,.sch).* *The error that I get in the log file is:* ** delete__442E> One or more atoms absent from MODEL: O:1976: C:1976: N:1977: CA:1977: delete__442E> One or more atoms absent from MODEL: O:1977: C:1977: N:1978: CA:1978:.................................................................................. ............................................................................................................ ..........................so on. ** *And the other error that it shows*: csrrng__299E> Atom index is out of bounds: 30677 30676 csrrng__299E> Atom index is out of bounds: 30680 30676 nselat__596E> Atom index is out of range (iatm,natm): 30680 30676 SOMEONE PLEASE SUGGEST A SOLUTION FOR WHY THE MODEL IS NOT ACCEPTING THE HETATOMS? Thanks Natasha

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alignment matrix
by Schulze, Diana 30 Jan '06

30 Jan '06

Dear all, I made a model with modeller and used the function auto_align() to get an automatic alignment. Now my question is the following: How can I find out which matrix (BLOSOM 60,...) was used to build this alignment? Sincerely, Diana Schulze

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Unexpected keyword argument
by Eva María Priego 25 Jan '06

25 Jan '06

Dear users, I'm trying to make two strands in my model (Modeller8v0 , Windows) I have search the FAQ and I tried one script found there, but I get this error: a= mymodel (env, alnfile='JP.ali', knows='JAN', 'sequence='B-1') a= mymodel (env, ) mymodel get an unexpected keyword argumen 'alnfile'. I don't know what to do. Can someone help me?. Thank you in advance. Eva Here is my script: #Make two STRANDS def mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND', residue_ids=('63', '67')) rsr.make(aln, restraint_type='STRAND', residue_ids=('134', '137')) log.verbose() env = environ() env.io.atom_files_directory = '' a.starting_model= 1 a.ending_model = 30 a = mymodel(env, alnfile='JP.ali', knowns='JAN', sequence='B-1') a.make()

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successive model building
by adak Nasiripour 21 Jan '06

21 Jan '06

dear all; I am going to build a model based on a multiple subunit membrane chanel(a five subunit homopantameric one); it is suggested that I build these kind of models in a "successive" manner, meaning:keeping the template multisubunit and running modeller with the target sequence; then again keeping the template subunits (all) along with the first and second target sequences; then again having template in hand with the dimer made, building the third subunit and so on... somebody guide me:1- what is the benefit of this successive step modelling? 2- how should I perform this? does anybody have an example file to show me how to add previous models to the current project? thanks. adak N. --------------------------------- Yahoo! Photos Showcase holiday pictures in hardcover Photo Books. You design it and well bind it!

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QUERY
by uday kumar 20 Jan '06

20 Jan '06

hi all, i want to model some of oGPCRs in humans,when i went for the similarity search using blast and fasta against PDB(to get template) ,the maximum similarity is only upto 32-35 for the corrwesponding entreis ,so want can i do ???can anyone sugest..

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about the installation of modeller8v1
by Shulin Zhuang 18 Jan '06

18 Jan '06

Dear All, I just install the modeller8v1 on SGI300 and I run the install script. At finally the message"Happy modeling!" "MODELLER Team, 2005" arise. At the bin directory, there are such commands as mod8v1_i386-intel8,mod8v1_iris4d..... but no mod8v1. For my machine is SGI300, the command that I should use is mod8v1_iris4d. Therefore after the installation , I set the environment at the .cshrc file: #Modeller setenv PATH $PATH\://usr/people/biomd/modeller/bin setenv KEY_MODELLER8v1 xxxx(the password) alias mod8v1 mod8v1_iris4d But when I run the examles at the automodel: run_tests It tells me that: Fatal error, MODINSTALL8v1 environment variables not set: incomplete installation. What is the error in my environment variables. How should I do. -- Shulin Zhuang Chemistry Department Zhejiang University PRC shulin.zhuang(a)gmail.com

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Advantages of manual protein sequence alignment between target and template [Very urgent please]
by rajesh rengaraj 17 Jan '06

17 Jan '06

Hello protein builders; I am new to the Homology modeling field, I have membrane protein as a target and I need to model this protein, because of less sequence identity I suppose to model this protein by manual protein sequence alignment between the target and template. Let me know the advantages of manual protein sequence alignment and by this whether it is possible to improve the structure of the target protein. I need some ideas regarding this issue. Any suggestions would be appreciated. With regards, Rajesh Rangaraj. Send instant messages to your online friends http://in.messenger.yahoo.com

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Re: modeller_usage Digest, Vol 5, Issue 7
by jo hanna 13 Jan '06

13 Jan '06

Hi I would like to ask a question re the check.py and prosa2003 analysis of my model In the model I am building the check.py script identifies a region int he modeller produced alignment where the distance is greater than 8 angstroms This region corresponds to an insertion in the sequence to be modelled which aligns with a helix region in the template. Using prosa to assess the quality of a model built with this alignment shows that the energy for this region is lower than that of the template (there is a peak in the template at this region of beta sheet of 0.7). adjusting the alignment to remove this insertion against the region of secondary structure, and to move it to a region of no secondary strcuture, provides a clean check.py result but a combined energy peak in prosa at the postion this previous insertion was which is 0.8 and matches the template. As I have mentioned in the template there is a helix located at this position, In the secondary strcuture for the sequence, thetre is no predicted helix in the corresponding region. Could anyone please give me any thoughts on this behaviour?! Thanks Jo On 1/6/06, modeller_usage-request(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. FW: Ligand clues and water blues (correction) (Mohsen, Al-Walid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Jan 2006 11:59:36 -0500 > From: "Mohsen, Al-Walid" <mohsaw(a)chp.edu> > Subject: [modeller_usage] FW: Ligand clues and water blues > (correction) > To: <modeller_usage(a)salilab.org> > Message-ID: <BFE40C28.2154%mohsaw(a)chp.edu> > Content-Type: text/plain; charset="US-ASCII" > > Sorry. when the .ini file is written it means Modeler accepted the > alignment, right or wrong, and the run will not stop for the error > mentioned > in your option 1. > > Best regards, > > Walid Mohsen > > > ------ Forwarded Message > From: <Mohsen>, Al-Walid <mohsaw(a)chp.edu> > Date: Fri, 06 Jan 2006 11:54:23 -0500 > To: <modeller_usage(a)salilab.org> > Conversation: Ligand clues and water blues > Subject: Re: Ligand clues and water blues > > Hi Jo, > > You have two messages and I am not sure where you are. I mentioned earlier > in my reply to replace the /...* with XXX* for the template and ...* for > the > model in your alignment file. It seems like you're still including the '/' > character, which is unnecessary at the end of the sequence and may cause > problems (shifts). The '/' is necessary to break the peptide sequence in > the > middle of the sequence, not at the end. IF you do a dimer for example you > need it there between the monomers, but NOT at the end. > > In option one, > > > this gives this error: > > rdabrk__290E> Number of residues in the alignment and pdb files are > > different: 517 516 > > For alignment entry: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > the error is real and you should look for where the problem is in the pdb > file vs the alignment file. As I understand it you should have the > residues > coordinates in the pdb file then two ligands AMP (515) and Mg (516), and > then one water molecule, which should be marked as HETATM with the number > 517. If this is the way it is and the second line of the template in > alignment file is: > > structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00 > > RKQLPEPDLTFXXX* > > and the XXX* is aligned with the ...* AFTER the .ini is written (see > below), > then you should not get this error, unless you deleted something (a > residue) > by mistake. > > In option 2: > > You MUST check the alignment file for shifts after you exe or start the > Modeler_Run AND the .ini file is written. Modeler 7 is known for > introducing > '-' into the sequence and things get messed up. This occurs near the '/' > character. > > In option 3: > > Everyone else can correct me, if I am wrong, but I do not see the problem > with water coming up as BLK. As long as it's in the proper position in the > 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. > If you do the XXX aligned with ... then all HETATM including water are > treated as HETATM and renamed BLK. > > In option 4: > > I would leave water_IO = on out. Do not assume that all the commands work > perfectly right. As I mentioned above Modeler 7 has this shift issues that > was not present in Modeler 6. > > Best regards, > > Walid Mohsen > > > > > From: <modeller_usage-request(a)salilab.org> > > Reply-To: <modeller_usage(a)salilab.org> > > Date: Fri, 6 Jan 2006 04:21:40 -0800 > > To: <modeller_usage(a)salilab.org> > > Subject: modeller_usage Digest, Vol 5, Issue 5 > > > > Send modeller_usage mailing list submissions to > > modeller_usage(a)salilab.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://salilab.org/mailman/listinfo/modeller_usage > > or, via email, send a message with subject or body 'help' to > > modeller_usage-request(a)salilab.org > > > > You can reach the person managing the list at > > modeller_usage-owner(a)salilab.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of modeller_usage digest..." > > > > > > Today's Topics: > > > > 1. modelling with water again (jo hanna) > > 2. Help needed (jo hanna) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 4 Jan 2006 00:33:28 +0000 > > From: jo hanna <jfhanna(a)gmail.com> > > Subject: [modeller_usage] modelling with water again > > To: modeller_usage(a)salilab.org > > Message-ID: > > <4b21263d0601031633p52f2b0dbid0d1190a1301f952(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello > > > > Many thanks for the advice Walid, I have done as you have suggested and > have > > made some progress but still am not seeing the behaviour that I am > > expecting. > > > > I have been using the pap format for the alignment as this has being > working > > better and have tried the following varied options in the top and align > > files, I should also mention that in my pdb i have the exact number of > > ligands(2), and single water that i would want to include in my model > > > > Option 1: > > remove water_io command from top file, > > try X for water and not w therefore at end of alignment > > structure = /..W > > and seqeunce = /... > > > > this gives this error: > > rdabrk__290E> Number of residues in the alignment and pdb files are > > different: 517 516 > > For alignment entry: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Option 2: > > water_io = on in top file, in alignment file, structure end aligmment = > /..X > > seqeunce end alignment = /... > > gives this error > > rdabrk__291E> Sequence difference between alignment and pdb : > > > > STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- > > 1 517 24 UNK 28 TIP3 LTF..X > > check_a_337E> Structure not read in: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Option 3: > > water_io = on in top file, end of alignments, strcuture = /..w seqeunce > = > > /... > > > > This combination creates a model but there is no mention in the logfile > of > > the BLK residues or of whether the water is accepted and in the final > model > > the water O is written as a BLK residue. From previoud posts i was > expecting > > a message in the log file re the TIP3 water and also for the model to > > contain a HOH or OH2 and not a BLK. > > > > Option 4: > > water_io = on in top file and end os alignments strcuture = > /..w seqeunce = > > /..w > > This once agaian produces the out of range error > > delete__443_> Restraints marked for deletion were removed. > > Total number of restraints before, now: 51247 47550 > > nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Any help would be greatly apprecaited. > > > > Thanks > > Jo > >

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adminaddress
by N.Arun Prasanna 12 Jan '06

12 Jan '06

Sir, Im not able to access subscribers list Admin id: prasanna(a)bits-pilani.ac.in password: modellerac Regards, Prasanna

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